Both Fink and MacPorts, on the other hand, install virtually an entire second world of software - parallel to the built-in Apple stuff - in their respective sub-directories (/sw for Fink and /opt/local for MacPorts).
If you install Getmail with MacPorts, for example, you instantly drag in a full Python installation as a dependency (even though OSX already has Python installed). Similarly, if you install Weechat with Perl support, MacPorts installs its own version of Perl to build Weechat against. There are pros and cons, I think, to the Homebrew and MacPorts/Fink methods, but they are very different.
I don't know the specific problems they had.
I agree that it may seems somewhat stupid now, but there was (and perhaps still is) a very good reason for installing them separately.
And even then, sadly the pretty decent versions don't get updated (OSX 10.6 comes with Python 2.6.1… 2.6.2 was released in April…), so you're essentially SOL between two versions of OSX.